RetrogeneDB ID: retro_hsap_8

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:27189703..27190450(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000175793
• Aliases: SFN, YWHAS
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSG00000134308
• Aliases: YWHAQ, 14-3-3, 1C5, HS1
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_hsap_8
ATGGAGAGAGCCAGTCTGATCCAGAAGGCCAAGCTGGCAGAGCAGGCCGAACGCTATGAGGACATGGCAGCCTTCATGAA
AGGCGCCGTGGAGAAGGGCGAGGAGCTCTCCTGCGAAGAGCGAAACCTGCTCTCAGTAGCCTATAAGAACGTGGTGGGCG
GCCAGAGGGCTGCCTGGAGGGTGCTGTCCAGTATTGAGCAGAAAAGCAACGAGGAGGGCTCGGAGGAGAAGGGGCCCGAG
GTGCGTGAGTACCGGGAGAAGGTGGAGACTGAGCTCCAGGGCGTGTGCGACACCGTGCTGGGCCTGCTGGACAGCCACCT
CATCAAGGAGGCCGGGGACGCCGAGAGCCGGGTCTTCTACCTGAAGATGAAGGGTGACTACTACCGCTACCTGGCCGAGG
TGGCCACCGGTGACGACAAGAAGCGCATCATTGACTCAGCCCGGTCAGCCTACCAGGAGGCCATGGACATCAGCAAGAAG
GAGATGCCGCCCACCAACCCCATCCGCCTGGGCCTGGCCCTGAACTTTTCCGTCTTCCACTACGAGATCGCCAACAGCCC
CGAGGAGGCCATCTCTCTGGCCAAGACCACTTTCGACGAGGCCATGGCTGATCTGCACACCCTCAGCGAGGACTCCTACA
AAGACAGCACCCTCATCATGCAGCTGCTGCGAGACAACCTGACACTGTGGACGGCCGACAACGCCGGGGAAGAGGGGGGC
GAGGCTCCCCAGGAGCCCCAGAGCTGA

Alignment

ORF - retro_hsap_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.85 %
• Parental protein coverage: 96.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTD
          ME...LIQKAKLAEQAERY.DMA..MK...E.G.ELS.EERNLLSVAYKNVVGG.R.AWRV.SSIEQK..
Retrocopy MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSN

Parental  T--SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDR
          ...S..K......YREKVE.EL...C.TVL.LLD..LI..A...ES.VFYLKMKGDY.RYLAEVA.GDD.
Retrocopy EEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDK

Parental  KQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNE
          K..ID....AYQEA.DISKKEM.PT.PIRLGLALNFSVF.YEI.N.PE.A..LAKT.FDEA.A.L.TL.E
Retrocopy KRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSE

Parental  DSYKDSTLIMQLLRDNLTLWTSDSAGEE
          DSYKDSTLIMQLLRDNLTLWT.D.AGEE
Retrocopy DSYKDSTLIMQLLRDNLTLWTADNAGEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	1.85 RPM	222.67 RPM
bodymap2_adrenal	0.55 RPM	187.66 RPM
bodymap2_brain	1.38 RPM	412.17 RPM
bodymap2_breast	4.20 RPM	164.17 RPM
bodymap2_colon	3.42 RPM	285.98 RPM
bodymap2_heart	0.00 RPM	165.36 RPM
bodymap2_kidney	1.01 RPM	231.44 RPM
bodymap2_liver	0.00 RPM	113.96 RPM
bodymap2_lung	27.23 RPM	247.98 RPM
bodymap2_lymph_node	0.16 RPM	193.85 RPM
bodymap2_ovary	0.31 RPM	341.01 RPM
bodymap2_prostate	5.66 RPM	307.38 RPM
bodymap2_skeletal_muscle	0.00 RPM	47.20 RPM
bodymap2_testis	0.32 RPM	283.83 RPM
bodymap2_thyroid	0.53 RPM	251.85 RPM
bodymap2_white_blood_cells	0.08 RPM	212.96 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_8 in 18 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	1:27189485..27189915
ENCFF002CFX	POLR2A	1:27189497..27189863
ENCFF002CGN	POLR2A	1:27189574..27189790
ENCFF002CJZ	POLR2A	1:27189456..27189921
ENCFF002CKX	POLR2A	1:27189525..27189818
ENCFF002CRK	POLR2A	1:27189397..27189921
ENCFF002CSY	POLR2A	1:27189355..27192285
ENCFF002CUP	POLR2A	1:27189500..27189816
ENCFF002CUQ	POLR2A	1:27189442..27189946
ENCFF002CZC	POLR2A	1:27189424..27189948
ENCFF002CZD	POLR2A	1:27189437..27189905
ENCFF002CZY	POLR2A	1:27189138..27189654
ENCFF002DAE	POLR2A	1:27189584..27189779
ENCFF002DAV	POLR2A	1:27189494..27189864
ENCFF002DAY	POLR2A	1:27189388..27190024
ENCFF002DBO	POLR2A	1:27189505..27189856
ENCFF002DBP	POLR2A	1:27189529..27189824
ENCFF002DBQ	POLR2A	1:27189555..27189783

EST

1 EST(s) were mapped to retro_hsap_8 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM744184	27189639	27190042	99.6	401	2	399

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_92828	981 libraries	277 libraries	188 libraries	40 libraries	343 libraries

The graphical summary, for retro_hsap_8 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_8 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3
Gorilla gorilla	retro_ggor_211
Pongo abelii	retro_pabe_103
Callithrix jacchus	retro_cjac_31
Mus musculus	retro_mmus_163
Oryctolagus cuniculus	retro_ocun_248
Bos taurus	retro_btau_86
Sus scrofa	retro_sscr_35
Canis familiaris	retro_cfam_233
Equus caballus	retro_ecab_31

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8 ,
Homo sapiens	ENSG00000164924	1 retrocopy	retro_hsap_549,
Homo sapiens	ENSG00000166913	4 retrocopies	retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	1.39 RPM
CEU_NA11930	1.69 RPM
CEU_NA12004	0.95 RPM
CEU_NA12400	3.40 RPM
CEU_NA12751	1.09 RPM
CEU_NA12760	0.58 RPM
CEU_NA12827	2.88 RPM
CEU_NA12872	0.90 RPM
CEU_NA12873	1.28 RPM
FIN_HG00183	0.52 RPM
FIN_HG00277	0.67 RPM
FIN_HG00315	2.24 RPM
FIN_HG00321	0.54 RPM
FIN_HG00328	0.43 RPM
FIN_HG00338	1.26 RPM
FIN_HG00349	1.51 RPM
FIN_HG00375	0.22 RPM
FIN_HG00377	1.13 RPM
FIN_HG00378	0.49 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	1.03 RPM
GBR_HG00114	0.45 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.60 RPM
GBR_HG00134	0.33 RPM
GBR_HG00137	0.47 RPM
GBR_HG00142	0.47 RPM
GBR_HG00143	0.51 RPM
TSI_NA20512	0.25 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	0.31 RPM
TSI_NA20532	1.87 RPM
TSI_NA20538	0.28 RPM
TSI_NA20756	0.23 RPM
TSI_NA20765	0.29 RPM
TSI_NA20771	0.91 RPM
TSI_NA20786	0.29 RPM
TSI_NA20798	0.65 RPM
YRI_NA18870	0.58 RPM
YRI_NA18907	0.45 RPM
YRI_NA18916	0.93 RPM
YRI_NA19093	0.23 RPM
YRI_NA19099	0.88 RPM
YRI_NA19114	0.31 RPM
YRI_NA19118	0.89 RPM
YRI_NA19213	0.29 RPM
YRI_NA19214	0.22 RPM
YRI_NA19223	0.60 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).